Protein structure

Proteins are amino acid chains, made up from 20 different L-α-amino acids, also referred to as residues, that fold into unique three-dimensional protein structures. The shape into a which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids. Below about 40 residues the term peptide is frequently used. A certain number of residues is necessary to perform a particular biochemical function, and around 40-50 residues appears to be the lower limit for a functional domain size. Protein sizes range from this lower limit to several thousand residues in multi-functional proteins. However, the current estimate for the average protein length is around 300 residues. Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a an actin filament. Large protein complexes with RNA are found in the ribosome particles, which are in fact 'ribozymes'.

Folds and motifs of protein structure

Despite that there are about 100,000 different proteins expressed in

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eukaryotic systems, there are much fewer different structural motifs and  folds, partly as a consequence of evolved pathways and mechansims. Motif in this sense refers to a small specific combination of secondary structural elements (such as helix-turn-helix). These elements are often called supersecondary structures. Fold refers to a global type of arrangement, like helix-bundle or β-barrel. Structure motifs usually consist of just a few elements, e.g. the 'helix-turn-helix' has just three. Note that while the spatial sequence of elements is the same in all instances of a motif, they may be encoded in any order within the underlying gene. Protein structural motifs often include loops of variable length and unspecified structure, which in effect create the "slack" necessary to bring together in space two elements that are not encoded by immediately adjacent DNA sequences in a gene. Note also that even when two genes encode secondary structural elements of a motif in the same order, nevertheless they may specify somewhat different sequences of amino acids. This is true not only because of the complicated relationship between tertiary and primary structure, but because the size of the elements varies from one protein and the next.

Related Topics:
Structural motif - Helix-turn-helix - Supersecondary structure - Helix-bundle - β-barrel - Gene - DNA sequence - Amino acid

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